Analysis of the apple tree rhizosphere and phylloplane microbiota revealed the presence of pathogenic and conditionally pathogenic micromycetes: Penicillium, Cladosporium, Fusarium, Mucor, Trichotecium, Alternaria. The application of microbial fertilizers (MFs)—Azafok, Enzymocid, and Nitragin—reduced their abundance in the soil. This occurred due to the beneficial bacteria contained in the biopreparations (Bacillus spp., Bacillus aryabhattai, Pseudomonas fluorescens, Bradyrhizobium japonicum), which possess fungicidal activity and the ability to improve the mineral nutrition of plants, thereby enhancing their immune status. Nitragin also reduced the colonization of leaves by pathogenic fungi. The greatest reduction in contamination was achieved by the combined application of MFs with foliar feeding using mineral substances, particularly when using Azafok. The influence of MFs on the state of the epiphytic microbiota is associated with their indirect action through the activation of the host plant’s functional activity and the stimulation of its defense mechanisms. The MFs introduced into the soil stimulated an increase in the content of nitrogen, phosphorus, potassium, and calcium in the leaves. We also noted the influence of MFs on modifying the effect of foliar feeding on the nutrient content in the leaves. The leaf nitrogen content with the combined application of soil-applied Azafok and FF was lower than with soil application alone. Furthermore, the use of foliar fertilizing reduced the phosphorus and potassium content in the leaves against the background of Azafok and Enzymocid, although the relative level of these nutrient contents remained very high. Only the application of foliar fertilizing against the background of Nitragin stimulated an increase in the phosphorus and potassium content in the leaves. Further research is needed to clarify the nature of this modification.

Sustainable agriculture aims to reduce environmental impacts and enhance the use of renewable natural resources to improve soil fertility and crop productivity. Mineral fertilizer application is a major source of environmental harm, and the intensification of apple production has led to fertilizer rates that may pose ecological risks. Microbial biofertilizers offer a promising means to partially replace chemical inputs, supporting the transition to sustainable horticulture. However, fertilizer efficiency depends on multiple factors, including orchard management systems and the genetic characteristics of scion–rootstock combinations. To evaluate the effects of microbial fertilizers (MFs) on the seasonal dynamics of leaf copper (Cu), molybdenum (Mo), and zinc (Zn) in different apple scion–rootstock combinations under conventional and high-density orchard systems, we established a field experiment in two commercial orchards (total area 2 ha). Azafok application resulted in the highest leaf Cu concentrations in both scion–rootstock combinations across phenological stages (5.54–6.39 mg kg⁻¹). Azafok also exerted a prolonged effect on leaf Zn in cultivar (cv.) ‘Rozhdestvenskoye’ grafted onto rootstock B396 in the high-density orchard (15.30 mg kg⁻¹). The highest leaf Zn in cv. ‘Veteran’ on rootstock B118 was recorded after Enzymocid application (19.97 mg kg⁻¹). For the ‘Rozhdestvenskoye’/B396 combination, the highest seasonal leaf Mo was observed with Azafok (0.635 mg kg⁻¹), whereas in the ‘Veteran’/B118 combination, it was highest following Nitragin application (1.079 mg kg⁻¹). Fertilizer application did not elevate fruit nutrient concentrations beyond permissible safety limits; all values remained within the normal ranges for the respective cultivars. To ensure stable MF effects, microbial consortia and strains with the most consistent and broad affect plant nutrition and status should be selected. Azafok and Enzymocid demonstrated strong antifungal effect in both the ‘Rozhdestvenskoye’/B396 and ‘Veteran’/B118 plantings. The antifungal effect of Nitragin was more pronounced in the ‘Rozhdestvenskoye’/B396 orchard.